Investigators have now boarded HMAS Ballarat, which is taking part in border protection operations. (file photo)

Australian Defence Force: Sarah Williams

The Defence Force says a number of sailors have been taken off HMAS Ballarat with investigators now aboard the ship after allegations crew members have been sexually assaulted.

The investigators include an Australian Defence Force Investigative Service (ADFIS) team and an officer from the Sexual and Misconduct and Response Office.

Defence will not say why or how many sailors have left the ship, or reveal their identity.

But it said on Sunday that they were now on mainland Australia after disembarking on Christmas Island.

It has taken several days for investigators to join the crew as the Anzac-class guided missile frigate is currently taking part in border protection operations.

Channel Ten had reported allegations that members on board HMAS Ballarat had been anally penetrated with objects including pens and water bottles as part of an initiation ritual.

Defence will not confirm the nature of the alleged behaviour being investigated.

A former Navy member who identified herself as Bridget told Channel Ten that sailors on board the ship have told her that young men are being attacked.

"People were set upon by members and stripped off and had things essentially put in their bums," she said.

"I think people are scared.

"If it happened in a normal workplace the police would be called, charges would be laid."

The Chief of Navy, Vice Admiral Ray Griggs, says the investigators will be continuing their probe into alleged inappropriate behaviour now that they are aboard the HMAS Ballarat.

"Navy will continue to be as open and transparent about this matter as we can be, but the investigation is now at the point where the ADFIS team needs to be able to get on with the job," he said in a statement.

"As such, no further public statements regarding these allegations will be made until the investigation is complete.

"I reiterate how seriously Navy takes allegations of this type and that inappropriate behaviour is neither consistent with our values nor tolerated in Navy."